Dropbox has recently changed its policy. I have updated the download links to get Assemble2.
I have fixed the popup window saying that you cannot reach the web server, even if you choose to use Docker.
By the way, you have to start Assemble2 from the command line, using one of the launch scripts (./launch_Assemble2_for_MacOSX.command for example). If you double-click on the jar, Assemble2 will not get the shell PATH and then will not be able to find Docker.
When i decided to connect Assemble2 to Web services, the idea was to free the user from installing the algorithms. But Web services have other limitations like difficulties to submit large data sets or accessibility (server down, stucked, behind a firewall,…). Consequently, i have decided to restore the ability to use algorithms installed on the user computer. And i think that this option is becoming interesting thanks to tools like Docker.
Here is the steps to follow to use the first release of Assemble2 powered by Docker:
- download the Assemble2.2 Development release. Now, you should see a Docker logo in the splash screen:
- install Docker on your computer
- install the Docker image fjossinet/assemble2, containing all the RNA algorithms configured. To do so, type the following command in a terminal:
docker pull fjossinet/assemble2
- by default, the local mode of Assemble2 is selected in the configuration window (File -> Configure -> Assemble2)
With the current Development release, you should be able to annotate 3D structures from PDB files, predict 2Ds from FASTA files and plot 2Ds from FASTA/BPSEQ/CT files. The ability to search for 3D fragments is not available for the time being. This is planed for the next release. Sorry for this delay.
I was very pleased to see Assemble2 highlighted in the last issue of Lab Times, the News Magazine for the European Life Sciences. In this article, available online or in its dead tree edition, Steven D. Buckingham reviews several bioinformatics tools allowing you to construct a 3D model for your favorite RNA molecule. Definitely, a must read!
The first versions of Assemble2 (RNAMLView, S2S and Assemble) were graphical tools dedicated to the rendering and manipulation of precomputed RNA structures. Now, Assemble2 is tightly linked to a server (public or self-deployed), hosting Web services, and deployable from a virtual machine. These Web services allow to automate RNA computations like sequence alignment, 2D prediction and 3D modeling. The initial idea was not to be exhaustive in terms of algorithms. In contrast to fully automated approaches, i wanted the RNA biologist to find in this tool his particular way of working: a first draft of alignment or structure followed by hours of manual changes to fit his assumptions and experimental data.
Within the last decade, the RNA field has grown rapidly: new RNA families, new RNA functions, new RNA algorithms, new RNA databases… The RNA biologist has now new needs and requirements. He wants to compute more, to visualize more, to compare more, to keep track of all his predictions and modifications. RNA complexes studied are becoming increasingly huge, and are made up of several partners. Several people can be involved in such studies. They need to split the work and to communicate. RNAs perform various functions, but are made with sequential, 2D and 3D patterns which are recurrent between the different RNA families. RNA biologists need to have access to a data warehouse hosted in their lab, allowing them to store, retrieve and share their data. In short, they need a laboratory information management system (LIMS) dedicated to RNA data, an RNA Science Toolbox. This idea is not new, but its fulfillment could be. Especially in the field of RNA.
I had two options to perform this goal: to add new features to Assemble2 or to further develop the Web server. I chose the second option. So, how will be structured this RNA Science toolbox?
First, we need to install and configure RNA algorithms to produce data. We need also to install and configure at least one database to store and retrieve the data produced by the users. This is the computing and data layer of our RNA Science Toolbox.
But having everything installed and configured at the same place is not enough. We need a way to communicate with all these “low-levels” tools in a more uniform way. The Bio* projects from the Open Bioinformatics Foundation provides such communication interfaces since a while. At the moment, i have developed my own solution in Python and it is named PyRNA. PyRNA is able to communicate with tools installed locally, but also with public databases (RFAM, NDB,…) and public Web services. PyRNA is lighter and more RNA oriented than BioPython. But i’m pretty sure that i will delegate the work to BioPython for more “classical” bioinformatics tasks. This Python library will be the middle layer of the toolbox.
The full installation and setup of all these components (algorithms, database, Python library,…) is a mess. This is where a virtual machine comes in play. Virtual machines allow to deploy a fully configured environment in a few easy steps. The RNA Science Toolbox is based on a Linux distribution to be deployed with the tool Vagrant. If we stop here, each user will need to install his own toolbox on his computer and will manage his own data warehouse. Futhermore, his way to do RNA Science will be restricted to the command-line: an efficient but limited way concerning visualization and interactivity with RNA data.
We can go further beyond. The Python library PyRNA contains an embedded Web server based on Tornado. This Web server already provides Web services (many more will come soon) and will offer interactive and graphical Web pages. These Web pages will allow to write interactive notebooks, in the same spirit as what you have with iPython, Beaker or Findings. The Web services will allow to connect non-Web based (native) tools like Assemble2. Consequently, a user would be able to write a Web notebook dedicated to the identification of new RNA 3D motifs, store them in the local database and use them through Assemble2 for the construction of a 3D model.
Or a user would be responsible to work on the identification of new RNA motifs in order to help others in the lab for the construction of 3D models.
With this blog post, i wanted to highlight the ideas that will guide my further developments. The project PyRNA has been renamed RNA Science Toolbox and it has now a twitter account. In parallel with the development of this toolbox, Assemble2 will also get new features to put them in synergy.
Next week, i will attend the 1st International Workshop on Virtual and Augmented Reality dedicated to Molecular Science (VARMS 2015):
The international IEEE Virtual Reality 2015 conference, through the VARMS workshop, gives researchers an excellent opportunity to:
- keep up to date with new approaches at the interface between Augmented and Virtual Reality, 3D User Interfaces and Video Games to popularize Molecular Science, both in research and teaching contexts,
- identify efforts to support the deeper integration of Virtual Reality techniques in the processes and practices of research laboratories and companies in the Molecular Science field, promoting the usefulness and usability of Virtual and Augmented Reality in Molecular Science, implying deep ergonomic analyses and user evaluations in the targeted field,
- highlight convincing success stories, thereby catalysing the use of Virtual and Augmented Reality in the targeted community, as actual research achievements that lead to decisive results in Molecular Science are still rare.
Here is my poster on Assemble2.
If you want to play with the new features available with version 1.2 before its stable release, go now to the downloads page. Please note that you will need Java 8 update 20 or greater to run it. Several features are still under development and could be buggy. Any feedback is welcome 😉